Document Detail


The protein folding transition state: insights from kinetics and thermodynamics.
MedLine Citation:
PMID:  20886966     Owner:  NLM     Status:  In-Process    
Abstract/OtherAbstract:
We perform extensive lattice Monte Carlo simulations of protein folding to construct and compare the equilibrium and the kinetic transition state ensembles of a model protein that folds to the native state with two-state kinetics. The kinetic definition of the transition state is based on the folding probability analysis method, and therefore on the selection of conformations with 0.4<P(fold)<0.6, while for the equilibrium characterization we consider conformations for which the evaluated values of several reaction coordinates correspond to the maximum of the free energy measured as a function of those reaction coordinates. Our results reveal a high degree of structural similarity between the ensembles determined by the two methods. However, the folding probability distribution of the conformations belonging to our definition of the equilibrium transition state (0.2<P(fold)<0.8) is broader than that displayed by the kinetic transition state.
Authors:
Rui D M Travasso; Patrícia F N Faísca; Antonio Rey
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  The Journal of chemical physics     Volume:  133     ISSN:  1089-7690     ISO Abbreviation:  J Chem Phys     Publication Date:  2010 Sep 
Date Detail:
Created Date:  2010-10-04     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0375360     Medline TA:  J Chem Phys     Country:  United States    
Other Details:
Languages:  eng     Pagination:  125102     Citation Subset:  IM    
Affiliation:
Departamento de Física, Centro de Física Computacional, Universidade de Coimbra, Coimbra 3004-516, Portugal. rui@lca.uc.pt
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